SMAT tool: Custom Master Pages

Hi

as per below SMAT's scanner report, if a site set with a custom masterpage (whether it is application or system master), it should appear in this report as issue

https://docs.microsoft.com/en-us/sharepointmigration/migration-assessment-scan-master-pages

However we found that one site with a custom masterpage for application/front , not appearing in the report. Anyone faced the same and knows any reason for it?